Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

how to use Multi-interval in GenomicsDBImport with gatk 4.0.6.0

I used the GenomicsDBImport with a interval list file and got a error like below.
So what is the correct way to use Multi-interval in GenomicsDBImport?

gatk version: 4.0.6.0

Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -Xms4g -jar /mnt/gatk/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar GenomicsDBImport -L test.intervals --genomicsdb-workspace-path ../RAW_VCF/my_database -V file1 -V file2 -V file3

02:57:15.591 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/workshop/xinchen.pan/test/gatk/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
02:57:15.772 INFO GenomicsDBImport - ------------------------------------------------------------
02:57:15.772 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.6.0
02:57:15.772 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
02:57:15.772 INFO GenomicsDBImport - Executing as on Linux v3.10.0-514.6.1.el7.x86_64 amd64
02:57:15.772 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_121-b13
02:57:15.773 INFO GenomicsDBImport - Start Date/Time: July 10, 2018 2:57:15 AM EDT
02:57:15.773 INFO GenomicsDBImport - ------------------------------------------------------------
02:57:15.773 INFO GenomicsDBImport - ------------------------------------------------------------
02:57:15.773 INFO GenomicsDBImport - HTSJDK Version: 2.16.0
02:57:15.773 INFO GenomicsDBImport - Picard Version: 2.18.7
02:57:15.773 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
02:57:15.773 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
02:57:15.773 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
02:57:15.773 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
02:57:15.774 INFO GenomicsDBImport - Deflater: IntelDeflater
02:57:15.774 INFO GenomicsDBImport - Inflater: IntelInflater
02:57:15.774 INFO GenomicsDBImport - GCS max retries/reopens: 20
02:57:15.774 INFO GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
02:57:15.774 INFO GenomicsDBImport - Initializing engine
02:57:18.389 INFO IntervalArgumentCollection - Processing 11228744 bp from intervals
02:57:18.437 INFO GenomicsDBImport - Done initializing engine
Created workspace ../RAW_VCF/my_database
02:57:18.583 INFO GenomicsDBImport - Vid Map JSON file will be written to ../RAW_VCF/my_database/vidmap.json
02:57:18.583 INFO GenomicsDBImport - Callset Map JSON file will be written to ../RAW_VCF/my_database/callset.json
02:57:18.583 INFO GenomicsDBImport - Complete VCF Header will be written to ../RAW_VCF/my_database/vcfheader.vcf
02:57:18.583 INFO GenomicsDBImport - Importing to array - ../RAW_VCF/my_database/genomicsdb_array
02:57:18.583 INFO ProgressMeter - Starting traversal
02:57:18.583 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
02:57:31.082 INFO GenomicsDBImport - Shutting down engine
[July 10, 2018 2:57:31 AM EDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=4116185088
Exception in thread "main" java.lang.StackOverflowError
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:95)
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:104)
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:104)
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:104)
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:104)
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:104)
at com.intel.genomicsdb.model.ImportConfig.isThereChromosomeIntervalIntersection(ImportConfig.java:104)

Issue · Github
by Geraldine_VdAuwera

Issue Number
4994
State
open
Last Updated
Assignee
Array

Best Answer

Answers

Sign In or Register to comment.